Mercurial > repos > iuc > trinity_define_clusters_by_cutting_tree
comparison define_clusters_by_cutting_tree.xml @ 0:acff96adcbec draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit b9a2194247d728ef4d5a3c5511aa6ea63e9b2bcb
author | iuc |
---|---|
date | Tue, 13 Dec 2016 14:43:00 -0500 |
parents | |
children | cd71eff81169 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:acff96adcbec |
---|---|
1 <tool id="trinity_define_clusters_by_cutting_tree" name="Partition genes into expression clusters" version="@WRAPPER_VERSION@.0"> | |
2 <description>after differential expression analysis using a Trinity assembly</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"> | |
7 <requirement type="package" version="2.30.0">bioconductor-biobase</requirement> | |
8 </expand> | |
9 <expand macro="stdio"/> | |
10 <command><![CDATA[ | |
11 | |
12 define_clusters_by_cutting_tree.pl | |
13 | |
14 -R '${rdata}' | |
15 | |
16 #if str( $method.method_selector ) == "--Ptree": | |
17 --Ptree ${method.ptree} | |
18 #else | |
19 #if str( $method.method_selector ) == "--Ktree": | |
20 --Ktree ${method.ktree} | |
21 #else | |
22 -K ${method.k} | |
23 #end if | |
24 #end if | |
25 | |
26 $additional_params.column_ordering | |
27 | |
28 && | |
29 mv *.clusters_fixed_*/* . | |
30 | |
31 ]]></command> | |
32 <inputs> | |
33 <param format="RData" name="rdata" argument="-R" type="data" label="RData file" help="RData file produced by 'Extract and cluster differentially expressed transcripts from a Trinity assembly' tool"/> | |
34 <conditional name="method"> | |
35 <param name="method_selector" type="select" label="Method for partitioning genes into clusters"> | |
36 <option value="--Ptree">Cut tree based on x percent of max(height) of tree</option> | |
37 <option value="--Ktree">Cut tree into K clusters</option> | |
38 <option value="-K">Define K clusters via k-means algorithm</option> | |
39 </param> | |
40 <when value="--Ptree"> | |
41 <param name="ptree" type="float" argument="--Ptree" value="20" label="Cut tree based on this percent of max(height) of tree" help="Give a percent value"/> | |
42 </when> | |
43 <when value="--Ktree"> | |
44 <param name="ktree" type="integer" argument="--Ktree" value="2" label="Cut tree into K clusters "/> | |
45 </when> | |
46 <when value="-K"> | |
47 <param name="k" type="integer" argument="-K" value="2" label="Define K clusters via k-means algorithm" help="This does not leverage the already hierarchically clustered genes, and instead uses a least-sum-of-squares method to define exactly k gene clusters."/> | |
48 </when> | |
49 </conditional> | |
50 <section name="additional_params" title="Additional Options" expanded="False"> | |
51 <param name="column_ordering" type="select" label="Column ordering in expression matrices" argument="--no_column_reordering / --lexical_column_ordering"> | |
52 <option value="">Order based on sample clustering</option> | |
53 <option value="--no_column_reordering">No reordering based on sample clustering</option> | |
54 <option value="--lexical_column_ordering">Reorder column names according to lexical ordering</option> | |
55 </param> | |
56 </section> | |
57 </inputs> | |
58 <outputs> | |
59 <collection name="expression_matrices" type="list" label="${tool.name} on ${on_string}: expression matrices for each cluster"> | |
60 <discover_datasets pattern="(?P<name>.+_log2_medianCentered_fpkm\.matrix)$" ext="tabular" /> | |
61 </collection> | |
62 <data format="pdf" name="cluster_plots" label="${tool.name} on ${on_string}: cluster plots" from_work_dir="my_cluster_plots.pdf"/> | |
63 </outputs> | |
64 <tests> | |
65 <test> | |
66 <param name="rdata" value="count/analyze_diff_expr/results.matrix.RData"/> | |
67 <conditional name="method"> | |
68 <param name="method_selector" value="--Ptree"/> | |
69 <param name="ptree" value="60"/> | |
70 </conditional> | |
71 <output_collection name="expression_matrices"> | |
72 <element name="subcluster_1_log2_medianCentered_fpkm.matrix" compare="sim_size" file="count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix"/> | |
73 <element name="subcluster_2_log2_medianCentered_fpkm.matrix" compare="sim_size" file="count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix"/> | |
74 </output_collection> | |
75 <output name="rdata" delta="100" compare="sim_size" file="count/define_clusters_by_cutting_tree/my_cluster_plots.pdf"/> | |
76 </test> | |
77 </tests> | |
78 <help> | |
79 <![CDATA[ | |
80 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. | |
81 This tool partitions the differentially expressed genes into gene clusters with similar expression patterns by one of several available methods, once differential expression analyses have been runned. It is a companion tool for the tool 'Extract and cluster differentially expressed transcripts from a Trinity assembly'. | |
82 | |
83 **Inputs** | |
84 | |
85 This tool uses the RData file produced by 'Extract and cluster differentially expressed transcripts from a Trinity assembly' tool. | |
86 | |
87 .. _Trinity: http://trinityrnaseq.github.io | |
88 ]]> | |
89 </help> | |
90 | |
91 <expand macro="citation" /> | |
92 </tool> |